Chemical Sciences: A Manual for CSIR-UGC National Eligibility Test for Lectureship and JRF/NMR spectra database

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Nuclear Magnetic Resonance (NMR) spectra database is an electronic repository of information concerning NMR spectra. The repository can be stored as a complete self contained data set or as an online repository that can be accessed and searched remotely. The form in which the data is stored ranges from line lists that can be graphically displayed to raw free induction decay (FID) data. The data is usually annotated in a way that correlates the spectral data with the related molecular structure.

Data format[edit]

Line list[edit]

The form in which most NMR is described in literature papers. It is common for databases to display line lists graphically in a manner that is similar to how processed spectra might appear. These line list however lack first and higher order splitting, satellites from low abundance isotopes like carbon or platinum, as well as the information concerning line width and other informative aspects of line shape. The advantage of a line list is that it requires a minimal amount of memory.

Processed image[edit]

Once an FID is processed into a spectrum it can be converted into an image that usually takes up less memory than the FID. This method requires more memory than a line list but supplies the user with considerably more information. The processed image has less information that a raw FID but it also take less memory and is easily displayed in browsers and requires no specially data handling software.

Raw free induction decay (FID) file[edit]

The data obtained when performing the experiment are stored according to the formatting preferences of the instrument manufacturer. This data format contains the most information and requires the most storage space. Since there are no applications for viewing FIDs in browsers the FID must be downloaded and subsequently processed. A variety of commercial and free of software programs allow users to process FID data into useful spectra once the FID file is stored on their computer.

Methods to search databases[edit]

Not all databases can be searched every way but these are search methods commonly available.

  • Compound name May include official IUPAC names and common names.
  • Molecular Formula Either an exact formula or a range.
  • Molecular Structure This method requires a molecular editor interface.
  • Registration number Commonly the CAS Registry Number but most databases also have their own numbering scheme.
  • Peak Range or other spectral characteristics The user numerically enters data related to a spectra of an unknown compound. This data is used to for compounds which share the shifts within specified constraints. This allows users to locate the exact compound or molecules with similar functional groups.
  • Spectra Search Software is used to search a database for spectra that resemble the a submitted spectra.

List of Databases[edit]

Spectral Database for Organic Compounds (SDBS)[edit]

A database developed and maintained by Japanese' National Institute of Advanced Industrial Science and Technology. The database includes 14700 1H NMR spectra and 13000 13C NMR spectra as well as FT-IR, Raman, ESR, and MS data. The data are stored and displayed as an image of the processed data. Annotation is achieved by a list of the chemical shifts correlated to letters which are also used to label a molecular line drawing. Access to the database is available free of charge for noncommercial use. Users are requested not to download more than 50 spectra and/or compound information in one day. Between 1997 and February of 2008 the database has been accessed more than 200 million times. T.Saito, K.Hayamizu, M.Yanagisawa and O.Yamamoto are attributed reproducibility for the NMR data.

ChemSpider[edit]

ChemSpider chemical database now accepts user submitted raw NMR data. The data in accepted in the JCAMP-DX format which can be actively viewed online with the JSpecView applet or the data can be downloaded for processing with other software packages. Its unclear the number of spectra included in the ChemSpider database.[1]

Biological Magnetic Resonance Data Bank (BoMagResBank or BMRB)[edit]

A Database sponsored by the Department of Biochemistry at the University of Wisconsin–Madison dedicated to Proteins, Peptides, Nucleic Acids, and other Biomolecules. Stores a large variety of raw NMR data. User modified and free to access online through a browser or FTP.

NMRshiftDB[edit]

A wiki-style database featuring graphically displayed line list data. The data are hosted by a distributed database with nodes at the Max Planck Institute of Chemical Ecology in Jena and Mainz University. Online access is free and user participation is encouraged. The data are available under the GNU FDL license. Contained 25141 measured spectra of, among other nuclei, 13C, 1H, 15N, 11B, 19F, 29Si, and 31P NMR as of February 2009.

ChemGate[edit]

A database developed and maintained by the publisher John Wiley & Sons. This database includes more than 700,000 NMR, IR and MS Spectra, spastics specific to the NMR spectra are not listed. The NMR data includes 1H,13C, 11B, 15N, 17O, 19F, 29Si, and 31P. The data are in the form of graphically displayed line lists. Access to the database can be purchased piecemeal or leased as the entire library through individual or group contracts.

Aldrich NMR Library[edit]

A portion of this database is still available in a three volume print version from Aldrich. The full electronic version includes a supplement of spectra not included in the paper version. In all, this database includes more that 15,000 compounds with the associated 300 MHz 1H and 75 MHz 13C spectra. The product includes the software necessary to view and handle the NMR data. This database can be purchased as a library through individual or group contracts. The spectra data appear to be stored as images of processed FID data.

ACDlabs[edit]

Advance Chemistry Development (ACD) labs chemoinformatics company which produces software for use in handling NMR data and predicting NMR spectra. ACD offers the Aldrich library as an add-on to their other NMR software products. It appears the ACD products may also include additional databases: HNMR DB, CNMR DB, FNMR DB, NNMR DB, and PNMR DB. These databases can be either be purchased or leased as libraries through individual or group contracts. The spectra data appears to be stored as images of processed FID data.

References[edit]